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- PDB-6bk5: Inactive choanoflagellate E3 ubiquitin ligase Cbl TKB -

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Basic information

Entry
Database: PDB / ID: 6bk5
TitleInactive choanoflagellate E3 ubiquitin ligase Cbl TKB
ComponentsUbiquitin Ligase Cbl
KeywordsSIGNALING PROTEIN / ubiquitin ligase / Cbl
Function / homology
Function and homology information


regulation of signaling / phosphotyrosine residue binding / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / cell surface receptor signaling pathway / calcium ion binding
Similarity search - Function
Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. / Adaptor protein Cbl, N-terminal domain superfamily ...Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. / Adaptor protein Cbl, N-terminal domain superfamily / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger, C3HC4 type (RING finger) / UBA-like superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
RING-type E3 ubiquitin transferase
Similarity search - Component
Biological speciesSalpingoeca rosetta (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.401 Å
AuthorsAmacher, J.F. / Kuriyan, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Jane Coffin Childs Memorial Fund for Medical ResearchPostdoctoral fellowship United States
CitationJournal: Protein Sci. / Year: 2018
Title: Phosphorylation control of the ubiquitin ligase Cbl is conserved in choanoflagellates.
Authors: Amacher, J.F. / Hobbs, H.T. / Cantor, A.C. / Shah, L. / Rivero, M.J. / Mulchand, S.A. / Kuriyan, J.
History
DepositionNov 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin Ligase Cbl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0622
Polymers41,0221
Non-polymers401
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.251, 115.251, 68.777
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-560-

HOH

21A-599-

HOH

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Components

#1: Protein Ubiquitin Ligase Cbl


Mass: 41021.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salpingoeca rosetta (strain ATCC 50818 / BSB-021) (eukaryote)
Strain: ATCC 50818 / BSB-021 / Gene: PTSG_09506 / Production host: Escherichia coli BL21(DE3) / Strain (production host): BL21(DE3) / References: UniProt: F2UL73
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2% (w/v) Tacsimate pH 7.0, 10% (w/v) polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999996 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999996 Å / Relative weight: 1
ReflectionResolution: 2.4→40.4 Å / Num. obs: 20844 / % possible obs: 99.84 % / Observed criterion σ(I): 1.5 / Redundancy: 2.04 % / CC1/2: 0.996 / Rrim(I) all: 0.075 / Rsym value: 0.097 / Net I/σ(I): 9.67
Reflection shellResolution: 2.401→2.54 Å / Redundancy: 2.03 % / Mean I/σ(I) obs: 1.73 / Num. unique obs: 5377 / CC1/2: 0.648 / Rrim(I) all: 0.527 / Rsym value: 0.677 / % possible all: 83.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.401→40.392 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.15
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 959 4.6 %Random selection
Rwork0.1668 ---
obs0.1688 20844 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.401→40.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2670 0 1 139 2810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072735
X-RAY DIFFRACTIONf_angle_d0.8493706
X-RAY DIFFRACTIONf_dihedral_angle_d17.0051640
X-RAY DIFFRACTIONf_chiral_restr0.048404
X-RAY DIFFRACTIONf_plane_restr0.005475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4009-2.52740.26971290.23522778X-RAY DIFFRACTION99
2.5274-2.68580.26931220.2082832X-RAY DIFFRACTION100
2.6858-2.89310.23891290.19732823X-RAY DIFFRACTION100
2.8931-3.18410.24041340.18662821X-RAY DIFFRACTION100
3.1841-3.64460.21121550.16842824X-RAY DIFFRACTION100
3.6446-4.59080.17341370.13792865X-RAY DIFFRACTION100
4.5908-40.39780.18671530.14572942X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.11060.3471-0.5023.3849-0.81523.84060.0775-0.1304-0.205-0.1174-0.5478-1.04170.02680.92850.23550.31620.02190.05190.42940.21620.5064-34.0215-9.7346-0.373
21.5259-1.0245-0.23212.77230.57431.04680.00320.00610.00980.077-0.0089-0.04380.01980.15980.01730.22230.0029-0.02040.19470.03420.1654-44.9234-26.003411.4159
33.8721-3.1309-0.83752.94141.7155.0808-0.1724-0.33830.04791.0470.1466-0.24820.28620.22960.00940.52030.0442-0.02170.31140.0750.2626-42.0035-37.7621.7387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 151 )
2X-RAY DIFFRACTION2chain 'A' and (resid 152 through 304 )
3X-RAY DIFFRACTION3chain 'A' and (resid 305 through 349 )

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